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GABPα Binding to Overlapping ETS and CRE DNA Motifs Is Enhanced by CREB1: Custom DNA Microarrays.

He X, Syed KS, Tillo D, Mann I, Weirauch MT, Vinson C - G3 (Bethesda) (2015)

Bottom Line: The DNA sequences include all 15-mers of the form (C)/GCGGA--CG-, the ETS↔CRE motif, and all single nucleotide polymorphisms (SNPs), and occurrences in the human and mouse genomes.CREB1 enhanced GABPα binding to the canonical ETS↔CRE motif CCGGAAGT two-fold, and up to 23-fold for several SNPs at the beginning and end of the ETS motif, which is suggestive of two separate and distinct allosteric mechanisms of cooperative binding.We show that the ETS-CRE array data can be used to identify regions likely cooperatively bound by GABPα and CREB1 in vivo, and demonstrate their ability to identify human genetic variants that might inhibit cooperative binding.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.

No MeSH data available.


Related in: MedlinePlus

GABPα binding to SNPs in two ETS↔CRE motifs. (A) GABPα-GST binding to 1960 features containing the ETS↔CRE 16-mer CCGGAAGTGACGTCAC and 48 SNPs on the ETS-CRE array. The first column of the figure contains 40 black spots representing GABPα-GST binding to the 40 features containing the consensus ETS↔CRE motif CCGGAAGTGACGTCAC. The rest of the columns represent 40 features for each of the 48 SNPs, as indicated. (B) GABPα-GST binding to 1960 features containing the weaker ETS↔CRE 16-mer GCGGAAGTGACGTCAC and 48 SNPs on the ETS-CRE array. (C) Histogram of the ratio of binding to the strong (CCGGAA) and weak (GCGGAA) ETS motif and SNPs. Horizontal dashed line indicates the ratio of binding to the strong (CCGGAA) and weak (GCGGAA) consensus ETS motif. Asterisk (*) indicates if the fold change is statistically significant when compared to the fold change of the strong motif (CCGGAA) (*P < 0.05; **P < 0.01).
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fig2: GABPα binding to SNPs in two ETS↔CRE motifs. (A) GABPα-GST binding to 1960 features containing the ETS↔CRE 16-mer CCGGAAGTGACGTCAC and 48 SNPs on the ETS-CRE array. The first column of the figure contains 40 black spots representing GABPα-GST binding to the 40 features containing the consensus ETS↔CRE motif CCGGAAGTGACGTCAC. The rest of the columns represent 40 features for each of the 48 SNPs, as indicated. (B) GABPα-GST binding to 1960 features containing the weaker ETS↔CRE 16-mer GCGGAAGTGACGTCAC and 48 SNPs on the ETS-CRE array. (C) Histogram of the ratio of binding to the strong (CCGGAA) and weak (GCGGAA) ETS motif and SNPs. Horizontal dashed line indicates the ratio of binding to the strong (CCGGAA) and weak (GCGGAA) consensus ETS motif. Asterisk (*) indicates if the fold change is statistically significant when compared to the fold change of the strong motif (CCGGAA) (*P < 0.05; **P < 0.01).

Mentions: We next examined GABPα-GST binding to the 40 replicate features (replicates) for the canonical ETS↔CRE motif (C/CGGAAGTGACGTCAC) and the 40 features (replicates) for each of the 48 SNPs (Figure 2). The variation in binding within the 40 features containing an identical DNA sequence is approximately two-fold (Figure 2A). GABPα-GST binds more strongly to the canonical ETS↔CRE motif (CCGGAAGT) than to any SNP. SNPs in the ETS core GGA trinucleotide (CCGGAAGT) uniformly decreased binding up to 27-fold. GABPα-GST binding to the SNPs for the five bases in bold (CCGGAAGT) at the beginning and end of the ETS motif is variable, consistent with known degeneracy in the GABPα recognition motif at these positions in motifs derived from in vitro (Badis et al. 2009) and in vivo (Valouev et al. 2008) data. There is no simple relationship between binding to SNPs based on their nucleotide type (i.e., whether they are purines or pyrimidines).


GABPα Binding to Overlapping ETS and CRE DNA Motifs Is Enhanced by CREB1: Custom DNA Microarrays.

He X, Syed KS, Tillo D, Mann I, Weirauch MT, Vinson C - G3 (Bethesda) (2015)

GABPα binding to SNPs in two ETS↔CRE motifs. (A) GABPα-GST binding to 1960 features containing the ETS↔CRE 16-mer CCGGAAGTGACGTCAC and 48 SNPs on the ETS-CRE array. The first column of the figure contains 40 black spots representing GABPα-GST binding to the 40 features containing the consensus ETS↔CRE motif CCGGAAGTGACGTCAC. The rest of the columns represent 40 features for each of the 48 SNPs, as indicated. (B) GABPα-GST binding to 1960 features containing the weaker ETS↔CRE 16-mer GCGGAAGTGACGTCAC and 48 SNPs on the ETS-CRE array. (C) Histogram of the ratio of binding to the strong (CCGGAA) and weak (GCGGAA) ETS motif and SNPs. Horizontal dashed line indicates the ratio of binding to the strong (CCGGAA) and weak (GCGGAA) consensus ETS motif. Asterisk (*) indicates if the fold change is statistically significant when compared to the fold change of the strong motif (CCGGAA) (*P < 0.05; **P < 0.01).
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4555227&req=5

fig2: GABPα binding to SNPs in two ETS↔CRE motifs. (A) GABPα-GST binding to 1960 features containing the ETS↔CRE 16-mer CCGGAAGTGACGTCAC and 48 SNPs on the ETS-CRE array. The first column of the figure contains 40 black spots representing GABPα-GST binding to the 40 features containing the consensus ETS↔CRE motif CCGGAAGTGACGTCAC. The rest of the columns represent 40 features for each of the 48 SNPs, as indicated. (B) GABPα-GST binding to 1960 features containing the weaker ETS↔CRE 16-mer GCGGAAGTGACGTCAC and 48 SNPs on the ETS-CRE array. (C) Histogram of the ratio of binding to the strong (CCGGAA) and weak (GCGGAA) ETS motif and SNPs. Horizontal dashed line indicates the ratio of binding to the strong (CCGGAA) and weak (GCGGAA) consensus ETS motif. Asterisk (*) indicates if the fold change is statistically significant when compared to the fold change of the strong motif (CCGGAA) (*P < 0.05; **P < 0.01).
Mentions: We next examined GABPα-GST binding to the 40 replicate features (replicates) for the canonical ETS↔CRE motif (C/CGGAAGTGACGTCAC) and the 40 features (replicates) for each of the 48 SNPs (Figure 2). The variation in binding within the 40 features containing an identical DNA sequence is approximately two-fold (Figure 2A). GABPα-GST binds more strongly to the canonical ETS↔CRE motif (CCGGAAGT) than to any SNP. SNPs in the ETS core GGA trinucleotide (CCGGAAGT) uniformly decreased binding up to 27-fold. GABPα-GST binding to the SNPs for the five bases in bold (CCGGAAGT) at the beginning and end of the ETS motif is variable, consistent with known degeneracy in the GABPα recognition motif at these positions in motifs derived from in vitro (Badis et al. 2009) and in vivo (Valouev et al. 2008) data. There is no simple relationship between binding to SNPs based on their nucleotide type (i.e., whether they are purines or pyrimidines).

Bottom Line: The DNA sequences include all 15-mers of the form (C)/GCGGA--CG-, the ETS↔CRE motif, and all single nucleotide polymorphisms (SNPs), and occurrences in the human and mouse genomes.CREB1 enhanced GABPα binding to the canonical ETS↔CRE motif CCGGAAGT two-fold, and up to 23-fold for several SNPs at the beginning and end of the ETS motif, which is suggestive of two separate and distinct allosteric mechanisms of cooperative binding.We show that the ETS-CRE array data can be used to identify regions likely cooperatively bound by GABPα and CREB1 in vivo, and demonstrate their ability to identify human genetic variants that might inhibit cooperative binding.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.

No MeSH data available.


Related in: MedlinePlus